We had the same problem. For me it is simply not clear what exactly the glas brain represents. But since we are normalizing to according templates, my guess is that it is most important how the resulting activation maps fit those templates.
All the best,
-Lucas
> -----Ursprüngliche Nachricht-----
> Von: "Ananth Narayanan" <[log in to unmask]>
> Gesendet: 09.09.08 17:10:04
> An: [log in to unmask]
> Betreff: Re: [SPM] Registration problem (Activation outside gla ss-brain region)
> I tried it on several images. When it overlaid this on the single subject
> T1s or the average T1, the activation stayed in the brain for this
> subject/session. I am going to repeat it for multiple subjects/sessions to
> verify that and post it soon.
>
> This makes me wonder, why is this so? What makes the activation go out of
> the glass brain? Thanks.
> - Ananth
>
> On Tue, 9 Sep 2008 07:55:09 +0200, Lucas Eggert <[log in to unmask]> wrote:
>
> >Dear Ananth,
> >
> >what happens when you overlay your activation map not simply on the glass
> brain, but on an according template, e.g. 'T1.nii'?
> >
> >Best regards,
> >Lucas
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: "Ananth Narayanan" <[log in to unmask]>
> >> Gesendet: 08.09.08 17:44:31
> >> An: [log in to unmask]
> >> Betreff: [SPM] Registration problem (Activation outside glass-brain region)
> >
> >
> >> I am running the analysis on data I acquired using the Philips 3T scanner.
> >>
> >> The sequence of steps I ran was
> >>
> >> Slice Timing
> >> Realign & Unwarp
> >> Coregister [Mean image from previous step]
> >> Normalize [to \spm\template\epi]
> >> Smooth [5 5 5]
> >>
> >> Most of the options were default.
> >>
> >> When I ran statistics on it (block design: 24 sec activation vs. 30 second
> >> rest, starting and ending with rest; FWE, p=0.05), activation appears
> >> outside the glass brain. I ran the statistics again (none, p=0.99) and the
> >> activated region went outside the glass brain as well.
> >>
> >> I assume this is some sort of a registration problem. Is there a way I can
> >> fix it? What exactly is going on? Thanks.
> >>
> >
> >
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